DIA/SWATH Course

Speakers

Ruedi Aebersold

Ruedi is professor at ETH Zurich. His research has focused on the
development of new technologies for quantitative proteomics and on applying them to challenging questions of contemporary life science research. In this area, the group has a worldwide standing and has pioneered a number of concepts and technologies that have transformed proteomics. These include the introduction of relative and absolute proteome quantification, the development of open source computational tools for the objective, statistically supported analysis of large proteomic datasets, the development of a method for the determination of the spatial organization of protein complexes and the development of targeted proteomic techniques such as Selected Reaction Monitoring and SWATH-MS.The concept of targeted proteomics has been selected Method of the Year 2012 by the journal Nature Methods.

Brendan MacLean

Brendan worked at Microsoft for eight years in the 1990s. Since leaving Microsoft, Brendan has worked in various companies and research institutions. For the last seven years he has worked as a senior software engineer within the MacCoss lab and been responsible for all aspects of design, development and support in creating the Skyline Targeted Proteomics Environment and its growing worldwide user community.

Olga Vitek

Olga is professor for statistics at the College of Computer and Information Science at Northeastern University. She develops statistical methods and algorithms for quantitative genomics, proteomics, metabolomics and ionomics. The methods optimize the design of investigations in these areas, and ensure accurate and objective interpretation of the resulting large and highly complex datasets.

Alexey Nesvizhskii

Alexey is an associate professor of the Department of Pathology and Computational Medicine & Bioinformatics at the University of Michigan in Ann Arbor. He also directs the Proteomics Resource Facility at University of Michigan. His laboratory is working in the area of bioinformatics, proteomics, and systems biology. Several widely used proteomic software tools were developed by him and his colleagues, like TPP, PeptideAtlas, SAINT, the CRAPome and DIA-UMPIRE.

Michael MacCoss

Michael is a professor at the Department of Genome Sciences at University of Washington in Seattle. His lab focuses on the development of approaches for mass spectrometry data analysis. Skyline was developed in his group as well as a number of other known software tools, like PECAN and Panorama.

Lukas Reiter

Lukas is working at the ETH spin-off Biognosys. After completing his PhD at the University of Zurich he was a PostDoc for one year and in parallel started at Biognosys, working on professionalizing the software development and applying it to novel acquisition techniques such as SWATH.

Christina Ludwig

Christina is the head of the proteomics facility at TU Munich. During her PostDoc in the Aebersold group in Zurich she focused on technical development projects related to targeted mass spectrometry, including SRM and SWATH MS. She was involved in projects aiming for the specific identification and quantification of post-translational modifications, in particular protein phosphorylation. Her second field of interest was the estimation of absolute protein abundances from label-free, targeted mass spectrometric data.

Course instructors

Ben Collins

Ben joined the Aebersold group in Autumn 2010 as postdoctoral researcher and established his own research group in March 2016 with the support of an SNF Ambiozione grant. His research focus is on the application of quantitative proteomics on the host-pathogen protein interactome of Mycobacterium tuberculosis.

Betty Friedrich-Grube

Betty joined the Aebersold group in May 2014 as a PhD student. Her research is focused on the application of SWATH-MS in clinical relevant research settings of various cancer types.

Isabell Bludau

Isabell joined the Aebersold group in July 2015 as a PhD student. She develops new algorithms for the qualitative and quantitative analysis of proteomics data, especially for SWATH-MS.

Nino Nikolovski

Nino joined the Aebersold group in May 2016 as a postdoctoral fellow, working towards high troughput discovery of membrane protein complexes.

Amir Banaei-Esfahani

Amir joined the Aebersold group in August 2015 as a PhD student. His research focuses on the investigation of multi-drug-resistant strains of Mycobacterium tuberculosis using SWATH-MS.